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          <img src="/2023/10/03/20231003-Xiaoyun/cover.png" srcset="/img/loading.gif" lazyload alt="Plant Commun. | 甘蓝型油菜功能基因组学研究的模式材料-小芸">
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          Plant Commun. | 甘蓝型油菜功能基因组学研究的模式材料-小芸
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      <a class="index-excerpt " href="/2023/10/03/20231003-Xiaoyun/" target="_self">
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          甘蓝型油菜（Brassica napus L.）是一种在世界范围内广泛种植的重要的油料作物，与模式植物拟南芥同属十字花科。甘蓝型油菜是由白菜和甘蓝在 ~7,500 年前种间杂交加倍后形成的，由于其祖先种白菜和甘蓝在物种形成过程中经历过多次基因组加倍事件，种间杂交加倍后又发生一系列基因保留和丢失事件，因此甘蓝型油菜基因组极其复杂，基因拷贝数高，这些特性极大地阻碍了油菜功能基因组学研究进展。 2023
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              <a href="/tags/%E7%94%98%E8%93%9D%E5%9E%8B%E6%B2%B9%E8%8F%9C/">#甘蓝型油菜</a>
            
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        <a href="/2023/09/20/20230920-tomatoCallusSpatialTranscriptomics/" target="_self">
          <img src="/2023/09/20/20230920-tomatoCallusSpatialTranscriptomics/cover.png" srcset="/img/loading.gif" lazyload alt="PNAS | 番茄愈伤组织芽再生的空间转录组图谱">
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          PNAS | 番茄愈伤组织芽再生的空间转录组图谱
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          再生芽的从头器官发生（De novo shoot organogenesis, DNSO）是植物再生的重要过程，包括愈伤组织的形成和再生芽的产生。拟南芥作为模式植物,其 DNSO 过程已经得到广泛研究,已经发现了许多关键的转录因子、激素和标记基因在这个过程中的调控作用。除此之外，光照可以促进再生芽形成,而光信号通路的核心组分 HY5 可以抑制再生芽的形成,这表明光促进再生芽形成可能不是依赖 HY5
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            <time datetime="2023-09-20 11:05" pubdate>
              2023-09-20
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              <a href="/tags/%E7%95%AA%E8%8C%84/">#番茄</a>
            
              <a href="/tags/%E6%A4%8D%E7%89%A9%E5%86%8D%E7%94%9F/">#植物再生</a>
            
              <a href="/tags/%E7%A9%BA%E9%97%B4%E8%BD%AC%E5%BD%95%E7%BB%84/">#空间转录组</a>
            
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        <a href="/2023/08/26/20230826-chatGPTforNetwork/" target="_self">
          <img src="/2023/08/26/20230826-chatGPTforNetwork/chatGPT.png" srcset="/img/loading.gif" lazyload alt="使用chatGPT绘制基因共表达网络图">
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          使用chatGPT绘制基因共表达网络图
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      <a class="index-excerpt " href="/2023/08/26/20230826-chatGPTforNetwork/" target="_self">
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          ChatGPT 是一款强大的语言模型，不仅可以回答问题和进行对话，还可以辅助编写代码。通过提供清晰的问题或指令，可以从 ChatGPT 获得代码段、算法示例以及编程建议。它支持多种编程语言和领域，为编程任务提供快速而可靠的帮助，无论是解决问题、学习新技术还是优化代码结构，ChatGPT 都能助你一臂之力。 我们以绘制基因共表达网络图为例展示 chatGPT 在写代码方面的作用。首先提出问题“绘制共
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            <time datetime="2023-08-26 21:50" pubdate>
              2023-08-26
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              <a href="/tags/R/">#R</a>
            
              <a href="/tags/%E7%BB%98%E5%9B%BE/">#绘图</a>
            
              <a href="/tags/chatGPT/">#chatGPT</a>
            
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        <a href="/2023/08/15/20230815-cucumberGraphBasedPanGenome/" target="_self">
          <img src="/2023/08/15/20230815-cucumberGraphBasedPanGenome/cucumber.png" srcset="/img/loading.gif" lazyload alt="Nat Commun. | 黄瓜 graph-based pangenome 与黄瓜农艺性状和驯化相关结构变异">
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        <a href="/2023/08/15/20230815-cucumberGraphBasedPanGenome/" target="_self">
          Nat Commun. | 黄瓜 graph-based pangenome 与黄瓜农艺性状和驯化相关结构变异
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      <a class="index-excerpt " href="/2023/08/15/20230815-cucumberGraphBasedPanGenome/" target="_self">
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          黄瓜(Cucumis sativus L.)是主要的蔬菜作物之一，也是植物性别决定和维管发育研究的模式植物。通过将自然群体重测序数据比对到单个基因组鉴定了黄瓜群体变异信息，以此研究了黄瓜的驯化历史和挖掘重要农艺性状相关基因。然而大片段结构变异（SV）的鉴定和研究仍然欠缺，需要进一步构建泛基因组增强 SV 的检测效果，进而促进黄瓜驯化和重要农艺性状相关 SV 研究。  11 个黄瓜品种的基因组组装
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              2023-08-15
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              <a href="/tags/%E5%9F%BA%E5%9B%A0%E7%BB%84/">#基因组</a>
            
              <a href="/tags/%E7%BB%93%E6%9E%84%E5%8F%98%E5%BC%82/">#结构变异</a>
            
              <a href="/tags/%E6%B3%9B%E5%9F%BA%E5%9B%A0%E7%BB%84/">#泛基因组</a>
            
              <a href="/tags/%E9%BB%84%E7%93%9C/">#黄瓜</a>
            
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        <a href="/2023/06/27/20230627-NewCircos/" target="_self">
          <img src="/2023/06/27/20230627-NewCircos/circos.png" srcset="/img/loading.gif" lazyload alt="R绘图 | 如何改变circos图中不同track中sector间的比例">
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      <h1 class="index-header">
        
        <a href="/2023/06/27/20230627-NewCircos/" target="_self">
          R绘图 | 如何改变circos图中不同track中sector间的比例
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      <a class="index-excerpt " href="/2023/06/27/20230627-NewCircos/" target="_self">
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          实际案例及问题 我们先看文章中的例子。在下图中最外两层分别表示了遗传连锁图和物理图（基因组），中间连线代表构图标记在遗传图和物理图上位置的对应关系。我们可以看到不同染色体间的长度比例和不同连锁图间的长度比例是相同的，但是这一点显然和实际情况不符。这幅图是由 circos 软件绘制，造成上述比例问题的原因可能是 circos 并不能改变不同 track 的比例，或者有改变比例的设置方法但作者并不知道
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            <time datetime="2023-06-27 20:11" pubdate>
              2023-06-27
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              <a href="/tags/R/">#R</a>
            
              <a href="/tags/%E7%BB%98%E5%9B%BE/">#绘图</a>
            
              <a href="/tags/circos/">#circos</a>
            
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          书接上文，我们已经了解 shiny 的主体结构，今天详细讲一讲用户界面（ui）部分。ui 是 shiny web 应用展示给用户的界面，那如何控制 ui 的布局并向其中插入图片、表格、文字等各种元素呢？ 布局 shiny使用 fluidPage 函数创建 ui 布局。 12345678ui &lt;- fluidPage(  titlePanel(&quot;title panel&quot;),
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          shiny 是一个创建交互式 web 应用程序的工具，有 R 和 python 版本，这里只涉及 R 版本。 安装 shiny 是一个 R 语言扩展包，安装方便： 1install.packages(&quot;shiny&quot;) 基本构成 一个 shiny 程序包含在一个文件夹中（即 shiny app 的工作目录，例如：newdir/），其中代码部分在文件夹内的一个叫 app.R 的 R
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